Puzzle 657
Puzzle 657 Blind Electron Density 3 same protein as Puzzle 602 Irc 308854 1354662732 E1 VC.png|Void Crushers E1 Irc 86905 1354662576 E1 VC.png|Void Crushers E1 Irc 86905 1354662500 E1 VC.png|Void Crushers E1 Irc 86905 1354662476 E1 VC.png|Void Crushers E1 Irc 184172 1354662745 E2 AD.png|Anthropic Dreams E2 Irc 184172 1354662364 E2 AD.png|Anthropic Dreams E2 Irc 184172 1354662302 E2 AD.png|Anthropic Dreams E2 Irc 308854 1354662622 E1 VC.png|Void Crushers E1 irc_341210_1354663718 S2 susume.png|Susume S2 irc_341210_1354663740 S2 susume.png|Susume S2 Irc 215720 1354662586 S7 pauldunn.png|pauldunn S7 Irc 215720 1354662573 S7 pauldunn.png|pauldunn S7 Irc 215720 1354662386 S7 pauldunn.png|pauldunn S7 Irc 215720 1354662360 S7 pauldunn.png|pauldunn S7 Irc 108474 1354662265 Bletchey park.png|Bletchly Park irc_42629_1354663255 S10 Madde.png|Madde s10 Irc 42629 1354662943 S10 Madde.png|Madde s10 Irc 269484 1354662727 S20 brow42.png|Brow42 S20 Irc 269484 1354662681 S20 brow42.png|Brow42 S20 00:02:02 Ad's top ones seem to map fairly well. 00:02:21 my backbone matches but my side chains don't 00:02:30 mine *seemed* too :) 00:02:52 yeah - i've seen that as well. many of the long chains do not have density around them. 00:03:44 one of the neat things about ED is you can see the flat circles for phen and tryp 00:04:04 I can see those flat circles in the ED in this puzzle, and the nearest phen is like 6 segments away 00:04:05 indeed. I had this one at some point 00:04:24 IMAGE: http://fold.it/portal/files/chatimg/irc_108474_1354662265.png 00:04:45 This is Galaxie's share. 00:04:59 I turned off the density at the end, too, and just tried to fold that 00:05:01 IMAGE: http://fold.it/portal/files/chatimg/irc_184172_1354662302.png 00:05:44 wow 00:05:46 there's lots of density there in the upper right in galaxie's picture....I could't fill it either 00:05:50 Evo, main contributer Steve 00:05:59 IMAGE: http://fold.it/portal/files/chatimg/irc_215720_1354662360.png 00:06:02 done by hand ? 00:06:03 IMAGE: http://fold.it/portal/files/chatimg/irc_184172_1354662364.png 00:06:25 IMAGE: http://fold.it/portal/files/chatimg/irc_215720_1354662386.png 00:06:41 my approach to ED currently is lots of tvdl rebuild, then hand fold loops back into the density and back to rebuild 00:06:50 @bp dont know i would think it was positioned mostly by hand at the start. 00:07:04 i'm impressed 00:07:55 IMAGE: http://fold.it/portal/files/chatimg/irc_86905_1354662476.png 00:07:58 i see paul's also has that bunch of density with no occupancy. 00:08:15 I reset once...the first time I tried to position the helices, then the sheets, but couldn't fit the sheets. 00:08:19 IMAGE: http://fold.it/portal/files/chatimg/irc_86905_1354662500.png 00:08:32 2nd try I started with sheets, particularly with the obvious hairpins, and placed the helices last 00:08:40 almost no cutpoint use 00:08:58 I used the prediction 00:08:58 IMAGE: http://fold.it/portal/files/chatimg/irc_86905_1354662540.png 00:09:17 then mapped it by counting helix winds, zigzags and used cutpoints 00:09:26 looks like VC and AD got almost exactly the same solution - only 6 points in it. 00:09:27 and did not work out that well 00:09:31 IMAGE: http://fold.it/portal/files/chatimg/irc_215720_1354662573.png 00:09:35 IMAGE: http://fold.it/portal/files/chatimg/irc_86905_1354662576.png 00:09:44 IMAGE: http://fold.it/portal/files/chatimg/irc_215720_1354662586.png 00:10:05 I am fairly shocked that you had the sidechains line up so well. 00:10:06 you could almost see the helices if you played with the threshold. 00:10:20 IMAGE: http://fold.it/portal/files/chatimg/irc_308854_1354662622.png 00:10:23 oh, I did see the helices and the sheets too 00:10:43 finally it worked Evo of Steves 00:10:55 MooMooMan, the sidechains fill in most of the density not filled in by the backbone. 00:11:19 IMAGE: http://fold.it/portal/files/chatimg/irc_269484_1354662681.png 00:11:56 there is still a bit at one point that seems unoccupied, right near the terminus of the protein that JPRED said was a helix but became a sheet.. 00:12:06 IMAGE: http://fold.it/portal/files/chatimg/irc_269484_1354662727.png 00:12:10 Steve, how on earth did you get the sidechains so well lined up ? 00:12:11 IMAGE: http://fold.it/portal/files/chatimg/irc_308854_1354662732.png 00:12:24 IMAGE: http://fold.it/portal/files/chatimg/irc_184172_1354662745.png 00:12:42 right at the top of the image i just posted. 00:14:22 I seemed to have EXTRA loops everywhere, and was missing loops nowhere 00:14:32 so I didn't know where to shift them 00:15:06 BP - using the ED mesh in wireframe mode. I then uploaded to group and we evo'd about 10 of them between us 00:15:16 I think there are extra ED regions that didn't get trimmed out when they tried to create an ED cloud for just one copy of the protein. 00:15:21 This ED data was far from perfect I think 00:15:41 <@Madde> IMAGE: http://fold.it/portal/files/chatimg/irc_42629_1354662943.png 00:15:45 they did take it from a repeating unit - thats probably the origin of the unmapped stuff. 00:15:47 I will try wireframe next time 00:15:49 I think they said that at one point 00:15:52 i'm really impressed 00:15:54 That it had extra 00:16:03 BP - I also use a repacking technique which is my secret weapon and speeds things up enormously 00:16:32 seems to work wonders 00:16:32 yes you got a high score very early on 00:17:02 The highest other score (ED match) was just above zero! 00:17:26 Yes Brow, I was about 3000 pts up and then the pack started to chase. It was a close run puzzle 00:17:33 hey, timo, could you real quick give the sum of Other subscore for your solution? 00:17:57 -1409.2537....... 00:18:19 what is Other subscore Brow ? 00:18:34 Best score on seg 107 0.022 00:18:38 cat's out of the bag now 00:18:42 mine is -2526.54 :( 00:18:50 look at the scores box as you move the protein BP... 00:18:59 other is the bonus/penalty for filling/unfilled ED 00:19:00 I think that is the subscore that Foldit uses to penalize or reward you for matching the ED cloud 00:19:14 I am sure of that 00:19:35 I'd like to know Steve's other score for the previous puzzle. 00:19:55 i'm puzzled with that 107 score 00:20:02 I'll go get pual if you wait a second 00:20:08 *paul 00:20:20 I'm pretty sure I had a +10 other score somewhere during folding 00:20:54 <@Madde> IMAGE: http://fold.it/portal/files/chatimg/irc_42629_1354663255.png 00:21:15 Me too Brow, but to prevent big negatives proved more fruitful 00:21:36 M3, which score should I look for on 107 ? 00:21:42 I was -1501 00:22:19 we think the match to the ED is in the Other score, but i am sure on one puzzle, i saw other parameters changing as i translated the protein. 00:22:31 -32 00:22:57 my best is 75 -1.6 00:23:20 How do I get the 'other' score from my puzzle folks ? 00:23:24 the problem is that they don't exactly excel at documentation of what they are doing... 00:23:40 -30 if I move it entirely out of the cloud 00:23:51 current.GetEnergySubscore(i,"other") 00:23:52 steve, use the TAB key to display details 00:24:18 aww, I missed the party 00:25:09 yep the TAB key gives me an individual residue OK, but how do I get the whole puzzle, other than writing an iterative script 00:25:22 I do not know 00:25:40 MooMooMan, I don't think translation is perfect for some reason. I can sometimes unstick wiggle by using the move tool 00:25:47 I think you have to write the recipe unless someone has shared one. 00:26:00 ah, so that is the name of that recipe 00:26:07 there are ceratinly recipes that give the sum of all subscores 00:26:18 Note that the Total score counts the other score twice 00:26:29 hey, maybe now would be a good time to plug my reciple :) 00:26:30 'OtherSubscore ' 00:26:51 if i could remember the name 00:27:10 Real score=total segment score+total other score 00:27:23 http://fold.it/portal/recipe/38634 00:27:26 and other score is also counted in the segment score 00:27:43 +8000 of course 00:27:59 thank you Timo 00:28:36 timo, I've never noticed other score is counted twice, you're positive? 00:28:37 IMAGE: http://fold.it/portal/files/chatimg/irc_341210_1354663718.png 00:28:58 IMAGE: http://fold.it/portal/files/chatimg/irc_341210_1354663740.png 00:29:03 nice job, Susume 00:29:28 here's the output of my script for just the other score: 00:29:30 ty 00:29:33 Because it is included in the segment score it is 00:29:34 Thanks Brow42 On blind ED 2 it's giving me +359.7 00:29:40 congrats to steveB, i just couldn't catch you 00:29:45 001111111000100012112211011 00000000000111123322211 212222222222110101112 333333321223334443322 1111112223222112122233 00:30:08 Thanks Susume - good old scrap - I enjoyed it 00:30:11 4 = best, 0 = worst 00:30:31 I didn't think to use this script during the puzzle though :( 00:30:56 Brow42 - how did you copy the data from the script window ? 00:31:22 I maintain a shortcut on my desktop to the default.scriptlog file 00:31:40 neat trick 00:32:44 On ED puzzle 2 I have ____444444444444444_444444________444444_____4444444444444______________4444444_______444____00 00:33:03 that's really impressive 00:33:21 in deafult script settings, all the 4's are the top 20% scoring 00:33:42 I had 3 4's :( 00:33:44 Nice script brow42 00:34:03 these are per-segment "other" scores? 00:34:19 default = sliding average 3 segments 00:34:23 my tottal other was -1420 00:35:37 what script, brow? 00:35:37 On ED3 I was -1407 00:35:46 wait no, default is 7 segment window 00:35:51 Region Scorer 00:36:06 They definately reduced the ED data quantity when they re-issued the puzzle 00:37:04 Shared some simple scripts for other scores 00:37:09 default settings on region scorer? 00:38:09 I only have five 4's Category:Puzzle Results